AMBER Archive (2008)

Subject: Re: AMBER: Jmol 11.7.1 pre-release version reads AMBER trajectory/coordinate files

From: Robert Hanson (hansonr_at_stolaf.edu)
Date: Wed Oct 08 2008 - 15:55:26 CDT

Francois,

Before I answer that, I have a few questions for you:

Q: Tell me more about what "display force field atom types" means. There is
an algorithm in Jmol that attempts to match an atom type specified in terms
of a PDB atom name to an element. It's used in both its mol2 reader and in
the AMBER topology file reader. So if it works in one (or doesn't!) then it
should (or won't!) in the other. I notice that even VMD makes mistakes
there, so I have to think not specifying the element is a flaw in the
topology file spec. Or am I missing something?

Q: Define "display." Do you mean "label by"? "select by"? "color by"?

Q: Jmol certainly reads mol2 files, and if those mol2 files have PDB residue
specifications, then it reads those. Is that what you mean?

Q: Jmol also reads cml files. But there is quite a bit of variation in that
standard. So I would have to look at the specific files you have in mind to
answer you. Can you send me (off-list) a few sample files?

Bob

On Wed, Oct 8, 2008 at 2:00 PM, FyD <fyd_at_q4md-forcefieldtools.org> wrote:

> Quoting Robert Hanson <hansonr_at_stolaf.edu>:
>
> Jmol/AMBER aficionados:
>> The latest pre-release of Jmol, Jmol 11.7.1 (
>> https://sourceforge.net/project/showfiles.php?group_id=23629) allows
>> reading
>> of AMBER topology and coordinate files.
>>
>> For those of you not familiar with Jmol (http://jmol.sourceforge.net,
>> http://chemapps.stolaf.edu/jmol), this open source Java applet and
>> application, though not as sophisticated as VMD -- and not in any way
>> intended to substitute for that program -- does allow quite extensive
>> molecular structure rendering capability, not just in the area of
>> molecular
>> dynamics.
>>
>> If you have any interest in using Jmol or helping with its development,
>> please do not hesitate to contact me or, especially, to join our user
>> group
>> (see http://jmol.sourceforge.net/project/).
>>
>
> Very nice...
>
> Can Jmol display force field atom types available in Tripos mol2 files,
> AMBER prmtop files or in CML files ? This would be great, & we would add
> this new feature in R.E.DD.B...
>
> Thank you, regards, Francois
>
>
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-- 
Robert M. Hanson
Professor of Chemistry
St. Olaf College
1520 St. Olaf Ave.
Northfield, MN 55057
http://www.stolaf.edu/people/hansonr
phone: 507-786-3107

If nature does not answer first what we want,
it is better to take what answer we get.

-- Josiah Willard Gibbs, Lecture XXX, Monday, February 5, 1900

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